Genome-scale approaches to resolving incongruence in molecular phylogenies

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.     

Skewed maturation of memory HIV-specific CD8 T lymphocytes

Understanding the lineage differentiation of memory T cells is a central question in immunology. We investigated this issue by analysing the expression of the chemokine receptor CCR7, which defines distinct subsets of naive and memory T lymphocytes with different homing and effector capacities and antiviral immune responses to HIV and cytomegalovirus. Ex vivo analysis of the expression of CD45RA and CCR7 antigens, together with in vitro analysis of the cell-division capacity of different memory CD8+ T-cell populations, identified four subsets of HIV- and CMV-specific CD8+ T lymphocytes, and indicated the following lineage differentiation pattern: CD45RA+ CCR7+ --> CD45RA- CCR7+ --> CD45RA- CCR7- --> CD45RA+ CCR7-. Here we demonstrate through analysis of cell division (predominantly restricted to the CCR7+ CD8+ T-cell subsets) that the differentiation of antigen-specific CD8+ T cells is a two-step process characterized initially by a phase of proliferation largely restricted to the CCR7+ CD8+ cell subsets, followed by a phase of functional maturation encompassing the CCR7- CD8+ cell subsets. The distribution of these populations in HIV- and CMV-specific CD8+ T cells showed that the HIV-specific cell pool was predominantly (70%) composed of pre-terminally differentiated CD45RA- CCR7- cells, whereas the CMV-specific cell pool consisted mainly (50%) of the terminally differentiated CD45RA+ CCR7- cells. These results demonstrate a skewed maturation of HIV-specific memory CD8+ T cells during HIV infection.     

Coherent manipulation of semiconductor quantum bits with terahertz radiation

Quantum bits (qubits) are the fundamental building blocks of quantum information processors, such as quantum computers. A qubit comprises a pair of well characterized quantum states that can in principle be manipulated quickly compared to the time it takes them to decohere by coupling to their environment. Much remains to be understood about the manipulation and decoherence of semiconductor qubits. Here we show that hydrogen-atom-like motional states of electrons bound to donor impurities in currently available semiconductors can serve as model qubits. We use intense pulses of terahertz radiation to induce coherent, damped Rabi oscillations in the population of two low-lying states of donor impurities in GaAs. Our observations demonstrate that a quantum-confined extrinsic electron in a semiconductor can be coherently manipulated like an atomic electron, even while sharing space with approximately 10(5) atoms in its semiconductor host. We anticipate that this model system will be useful for measuring intrinsic decoherence processes, and for testing both simple and complex manipulations of semiconductor qubits.     

Dengue-like viruses isolated by an improved method

Zusammenfassung Aus Seren von Dengue-Fieberkranken (Epidemie 1963) wurden zwei «Dengue-like» Viren isoliert. Die Isolierung der Stämme gelang in Bristol-HeLa-Zellen, die mit dem LKB 6300 A Ultrafilter dargestellt wurden. Die Identifizierung der Viren erfolgte mit der Reaktion der Komplementbindung.